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Aliases for TARDBP Gene

Aliases for TARDBP Gene

  • TAR DNA Binding Protein 2 3 5
  • TDP-43 3 4
  • TAR DNA-Binding Protein 43 3
  • TAR DNA-Binding Protein-43 3
  • ALS10 3
  • TDP43 4

External Ids for TARDBP Gene

Previous GeneCards Identifiers for TARDBP Gene

  • GC01P011033
  • GC01P010916
  • GC01P010682
  • GC01P010782
  • GC01P011006
  • GC01P010224
  • GC01P011072

Summaries for TARDBP Gene

Entrez Gene Summary for TARDBP Gene

  • HIV-1, the causative agent of acquired immunodeficiency syndrome (AIDS), contains an RNA genome that produces a chromosomally integrated DNA during the replicative cycle. Activation of HIV-1 gene expression by the transactivator Tat is dependent on an RNA regulatory element (TAR) located downstream of the transcription initiation site. The protein encoded by this gene is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. A similar pseudogene is present on chromosome 20. [provided by RefSeq, Jul 2008]

GeneCards Summary for TARDBP Gene

TARDBP (TAR DNA Binding Protein) is a Protein Coding gene. Diseases associated with TARDBP include Amyotrophic Lateral Sclerosis 10 With Or Without Frontotemporal Dementia and Amyotrophic Lateral Sclerosis 1. Among its related pathways are Neuroscience. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and DNA binding transcription factor activity. An important paralog of this gene is HNRNPDL.

UniProtKB/Swiss-Prot for TARDBP Gene

  • DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat. Stabilizes the low molecular weight neurofilament (NFL) mRNA through a direct interaction with the 3 UTR.

Gene Wiki entry for TARDBP Gene

Additional gene information for TARDBP Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TARDBP Gene

Genomics for TARDBP Gene

GeneHancer (GH) Regulatory Elements for TARDBP Gene

Promoters and enhancers for TARDBP Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I011011 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 570.9 +0.7 745 3.4 HDGF CLOCK SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 TARDBP ENSG00000277726 ENSG00000226849 CLCN6 EXOSC10 FBXO44 DFFA MASP2 ANGPTL7 ENSG00000271895
GH01I011907 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 57.5 +896.5 896453 3.1 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 RNU5E-1 RNU5E-4P TARDBP UBIAD1 ENSG00000226849 CLCN6 VPS13D SNORA59A MFN2 EXOSC10
GH01I010790 Promoter/Enhancer 3.3 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 35.6 -218.5 -218531 6.4 PKNOX1 ARID4B NEUROD1 SIN3A ZNF2 YY1 ZNF213 ZNF548 KLF13 SP3 CASZ1 TARDBP ANGPTL7 ENSG00000226849 CLSTN1 UBIAD1 FBXO44 EXOSC10 GC01P010673
GH01I010662 Enhancer 2.5 VISTA UCNEbase FANTOM5 Ensembl ENCODE dbSUPER 37.7 -335.8 -335845 28 PKNOX1 FOXA2 ZFP64 ARID4B NEUROD1 SIN3A FEZF1 DMAP1 ZNF2 ZNF213 TARDBP ENSG00000226849 EXOSC10 MTOR ENSG00000271895 C1orf127 DFFA PGD RBP7 CASZ1
GH01I011478 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 36.5 +466.9 466875 1 CLOCK ATF1 SIN3A ZNF48 ZNF766 GLIS2 ZNF213 E2F8 ZNF207 ZNF143 DISP3 TARDBP ENSG00000226849 EXOSC10 CLCN6 MTHFR LINC01647
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TARDBP on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TARDBP gene promoter:

Genomic Locations for TARDBP Gene

Genomic Locations for TARDBP Gene
chr1:11,012,344-11,026,420
(GRCh38/hg38)
Size:
14,077 bases
Orientation:
Plus strand
chr1:11,072,414-11,085,796
(GRCh37/hg19)

Genomic View for TARDBP Gene

Genes around TARDBP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TARDBP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TARDBP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TARDBP Gene

Proteins for TARDBP Gene

  • Protein details for TARDBP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13148-TADBP_HUMAN
    Recommended name:
    TAR DNA-binding protein 43
    Protein Accession:
    Q13148
    Secondary Accessions:
    • A4GUK4
    • A4GUK5
    • A4GUK6
    • B2R629
    • B4DJ45
    • E2PU12
    • Q53H27
    • Q6FI92
    • Q96DJ0

    Protein attributes for TARDBP Gene

    Size:
    414 amino acids
    Molecular mass:
    44740 Da
    Quaternary structure:
    • Homodimer. Interacts with BRDT (By similarity). Binds specifically to pyrimidine-rich motifs of TAR DNA and to single stranded TG repeated sequences. Binds to RNA, specifically to UG repeated sequences with a minimun of six contiguous repeats. Interacts with ATNX2; the interaction is RNA-dependent (PubMed:20740007). Interacts with MATR3 (PubMed:24686783). Interacts with UBQLN2 (PubMed:23541532). Interacts with HNRNPA2B1 (PubMed:19429692).
    SequenceCaution:
    • Sequence=ABO32290.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305}; Sequence=ABO32292.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TARDBP Gene

    Alternative splice isoforms for TARDBP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TARDBP Gene

Post-translational modifications for TARDBP Gene

  • Cleaved to generate C-terminal fragments in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU.
  • Hyperphosphorylated in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU.
  • Ubiquitinated in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU.
  • Ubiquitination at isoforms=95, isoforms=102, posLast=114114, posLast=160160, and posLast=181181

No data available for DME Specific Peptides for TARDBP Gene

Domains & Families for TARDBP Gene

Gene Families for TARDBP Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for TARDBP Gene

Graphical View of Domain Structure for InterPro Entry

Q13148

UniProtKB/Swiss-Prot:

TADBP_HUMAN :
  • The RRM domains can bind to both DNA and RNA.
Domain:
  • The RRM domains can bind to both DNA and RNA.
genes like me logo Genes that share domains with TARDBP: view

Function for TARDBP Gene

Molecular function for TARDBP Gene

UniProtKB/Swiss-Prot Function:
DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat. Stabilizes the low molecular weight neurofilament (NFL) mRNA through a direct interaction with the 3 UTR.

Phenotypes From GWAS Catalog for TARDBP Gene

Gene Ontology (GO) - Molecular Function for TARDBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding IDA 7745706
GO:0003700 DNA binding transcription factor activity TAS 7745706
GO:0003723 RNA binding IEA,IDA 11285240
genes like me logo Genes that share ontologies with TARDBP: view
genes like me logo Genes that share phenotypes with TARDBP: view

Human Phenotype Ontology for TARDBP Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TARDBP Gene

MGI Knock Outs for TARDBP:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TARDBP Gene

Localization for TARDBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for TARDBP Gene

Nucleus. Note=In patients with frontotemporal lobar degeneration and amyotrophic lateral sclerosis, it is absent from the nucleus of affected neurons but it is the primary component of cytoplasmic ubiquitin-positive inclusion bodies.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TARDBP gene
Compartment Confidence
nucleus 5
cytosol 3
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
lysosome 2
extracellular 1
golgi apparatus 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TARDBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 11285240
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with TARDBP: view

Pathways & Interactions for TARDBP Gene

SuperPathways for TARDBP Gene

SuperPathway Contained pathways
1 Neuroscience
genes like me logo Genes that share pathways with TARDBP: view

Pathways by source for TARDBP Gene

1 Cell Signaling Technology pathway for TARDBP Gene

Gene Ontology (GO) - Biological Process for TARDBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001933 negative regulation of protein phosphorylation IMP 18305152
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II TAS 7745706
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with TARDBP: view

No data available for SIGNOR curated interactions for TARDBP Gene

Drugs & Compounds for TARDBP Gene

(1) Additional Compounds for TARDBP Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TARDBP: view

Transcripts for TARDBP Gene

Unigene Clusters for TARDBP Gene

TAR DNA binding protein:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TARDBP Gene

No ASD Table

Relevant External Links for TARDBP Gene

GeneLoc Exon Structure for
TARDBP
ECgene alternative splicing isoforms for
TARDBP

Expression for TARDBP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TARDBP Gene

Protein differential expression in normal tissues from HIPED for TARDBP Gene

This gene is overexpressed in Nasal epithelium (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TARDBP Gene



Protein tissue co-expression partners for TARDBP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TARDBP Gene:

TARDBP

SOURCE GeneReport for Unigene cluster for TARDBP Gene:

Hs.300624

mRNA Expression by UniProt/SwissProt for TARDBP Gene:

Q13148-TADBP_HUMAN
Tissue specificity: Ubiquitously expressed. In particular, expression is high in pancreas, placenta, lung, genital tract and spleen.

Evidence on tissue expression from TISSUES for TARDBP Gene

  • Nervous system(5)
  • Liver(4.5)
  • Kidney(3.4)
  • Blood(3.3)
  • Lung(3.3)
  • Eye(2.7)
  • Muscle(2.7)
  • Intestine(2.5)
  • Pancreas(2.5)
  • Skin(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TARDBP Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • epiglottis
  • face
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • pharynx
  • skull
  • tongue
  • vocal cord
Thorax:
  • bronchus
  • clavicle
  • esophagus
  • heart
  • lung
  • scapula
  • trachea
Abdomen:
  • biliary tract
  • liver
  • stomach
Limb:
  • arm
  • digit
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • shin
  • shoulder
  • thigh
  • toe
  • upper limb
General:
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with TARDBP: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for TARDBP Gene

Orthologs for TARDBP Gene

This gene was present in the common ancestor of animals.

Orthologs for TARDBP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TARDBP 33 34
  • 99.52 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TARDBP 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia TARDBP 33 34
  • 92.75 (n)
mouse
(Mus musculus)
Mammalia Tardbp 33 16 34
  • 90.34 (n)
dog
(Canis familiaris)
Mammalia TARDBP 33 34
  • 89.94 (n)
oppossum
(Monodelphis domestica)
Mammalia TARDBP 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves TARDBP 33 34
  • 82.45 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia tardbp 33
  • 76.49 (n)
MGC75857 33
African clawed frog
(Xenopus laevis)
Amphibia tardbp-prov 33
zebrafish
(Danio rerio)
Actinopterygii tardbpl 34
  • 76 (a)
OneToMany
tardbp 33 34
  • 70.56 (n)
wufb77f02 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.3538 33
fruit fly
(Drosophila melanogaster)
Insecta TBPH 35 34
  • 56 (a)
CG7804 35 34
  • 54 (a)
worm
(Caenorhabditis elegans)
Secernentea F44G4.4 35
  • 38 (a)
tdp-1 34
  • 30 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10473 34
  • 44 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3080 33
Species where no ortholog for TARDBP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TARDBP Gene

ENSEMBL:
Gene Tree for TARDBP (if available)
TreeFam:
Gene Tree for TARDBP (if available)

Paralogs for TARDBP Gene

Paralogs for TARDBP Gene

genes like me logo Genes that share paralogs with TARDBP: view

Variants for TARDBP Gene

Sequence variations from dbSNP and Humsavar for TARDBP Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1033638 benign, Amyotrophic Lateral Sclerosis, Dominant, MASP2 deficiency, Frontotemporal dementia 11,026,660(+) A/G genic_downstream_transcript_variant, intron_variant
rs1033751502 uncertain-significance, Frontotemporal dementia, Amyotrophic Lateral Sclerosis, Dominant 11,024,683(+) C/T 3_prime_UTR_variant, intron_variant
rs11121679 benign, Frontotemporal dementia 11,012,634(+) G/A 5_prime_UTR_variant
rs114897688 likely-benign, MASP2 deficiency, Frontotemporal dementia, Amyotrophic Lateral Sclerosis, Dominant 11,024,985(+) A/G 3_prime_UTR_variant, intron_variant
rs115750484 likely-benign, Frontotemporal dementia, Amyotrophic Lateral Sclerosis, Dominant 11,026,701(+) G/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TARDBP Gene

Variant ID Type Subtype PubMed ID
nsv945768 CNV duplication 23825009
nsv832425 CNV loss 17160897
nsv545407 CNV gain 21841781

Variation tolerance for TARDBP Gene

Residual Variation Intolerance Score: 25.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.08; 1.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TARDBP Gene

Human Gene Mutation Database (HGMD)
TARDBP
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TARDBP

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TARDBP Gene

Disorders for TARDBP Gene

MalaCards: The human disease database

(48) MalaCards diseases for TARDBP Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TADBP_HUMAN
  • Amyotrophic lateral sclerosis 10 (ALS10) [MIM:612069]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases. {ECO:0000269 PubMed:18288693, ECO:0000269 PubMed:18309045, ECO:0000269 PubMed:18372902, ECO:0000269 PubMed:18396105, ECO:0000269 PubMed:18438952, ECO:0000269 PubMed:19224587, ECO:0000269 PubMed:19350673, ECO:0000269 PubMed:19655382, ECO:0000269 PubMed:19695877, ECO:0000269 PubMed:20740007, ECO:0000269 PubMed:21220647, ECO:0000269 PubMed:21418058, ECO:0000269 PubMed:22456481}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TARDBP

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TARDBP: view

No data available for Genatlas for TARDBP Gene

Publications for TARDBP Gene

  1. High frequency of TARDBP gene mutations in Italian patients with amyotrophic lateral sclerosis. (PMID: 19224587) Corrado L … D'Alfonso S (Human mutation 2009) 3 4 22 44 58
  2. Cloning and characterization of a novel cellular protein, TDP-43, that binds to human immunodeficiency virus type 1 TAR DNA sequence motifs. (PMID: 7745706) Ou SH … Gaynor RB (Journal of virology 1995) 2 3 4 22 58
  3. Association between novel TARDBP mutations and Chinese patients with amyotrophic lateral sclerosis. (PMID: 20082726) Xiong HL … Wu ZY (BMC medical genetics 2010) 3 22 44 58
  4. Neuronal inclusion protein TDP-43 has no primary genetic role in FTD and ALS. (PMID: 18068872) Gijselinck I … Cruts M (Neurobiology of aging 2009) 3 22 44 58
  5. Genetic association analysis between TDP-43 polymorphisms and Alzheimer's disease in a Japanese population. (PMID: 19851068) Shibata N … Arai H (Dementia and geriatric cognitive disorders 2009) 3 22 44 58

Products for TARDBP Gene

Sources for TARDBP Gene

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